Variant chr14-77279774-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_013382.7(POMT2):c.1891+49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 1,567,636 control chromosomes in the GnomAD database, including 3,034 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 208 hom., cov: 32)

Exomes 𝑓: 0.059 ( 2826 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

POMT2 (HGNC:19743): (protein O-mannosyltransferase 2) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT1 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS).[provided by RefSeq, Oct 2008]

POMT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 14-77279774-G-A is Benign according to our data. Variant chr14-77279774-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 260298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMT2	NM_013382.7 linkuse as main transcript	c.1891+49C>T		intron_variant		ENST00000261534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMT2	ENST00000261534.9 linkuse as main transcript	c.1891+49C>T		intron_variant		1	NM_013382.7	P1	Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.0418

AC:

6361

AN:

152066

Hom.:

208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.0354

Gnomad ASJ

AF:

0.0311

Gnomad EAS

AF:

0.000968

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.0501

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0647

Gnomad OTH

AF:

0.0402

GnomAD3 exomes

AF:

0.0414

AC:

8002

AN:

193232

Hom.:

230

AF XY:

0.0410

AC XY:

4299

AN XY:

104872

show subpopulations

Gnomad AFR exome

AF:

0.0104

Gnomad AMR exome

AF:

0.0268

Gnomad ASJ exome

AF:

0.0279

Gnomad EAS exome

AF:

0.000138

Gnomad SAS exome

AF:

0.0102

Gnomad FIN exome

AF:

0.0465

Gnomad NFE exome

AF:

0.0684

Gnomad OTH exome

AF:

0.0436

GnomAD4 exome

AF:

0.0585

AC:

82813

AN:

1415452

Hom.:

2826

Cov.:

AF XY:

0.0571

AC XY:

40141

AN XY:

702542

show subpopulations

Gnomad4 AFR exome

AF:

0.00913

Gnomad4 AMR exome

AF:

0.0286

Gnomad4 ASJ exome

AF:

0.0267

Gnomad4 EAS exome

AF:

0.000211

Gnomad4 SAS exome

AF:

0.0110

Gnomad4 FIN exome

AF:

0.0432

Gnomad4 NFE exome

AF:

0.0690

Gnomad4 OTH exome

AF:

0.0462

GnomAD4 genome

AF:

0.0418

AC:

6361

AN:

152184

Hom.:

208

Cov.:

AF XY:

0.0412

AC XY:

3063

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0115

Gnomad4 AMR

AF:

0.0354

Gnomad4 ASJ

AF:

0.0311

Gnomad4 EAS

AF:

0.000970

Gnomad4 SAS

AF:

0.00850

Gnomad4 FIN

AF:

0.0501

Gnomad4 NFE

AF:

0.0647

Gnomad4 OTH

AF:

0.0398

Alfa

AF:

0.0462

Hom.:

Bravo

AF:

0.0402

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 01, 2017	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.4

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over